Predicting the onset of DNA supercoiling using a non-linear hemitropic elastic rod

Elastic rod models provide a means to interpret single molecule DNA experiments as well as predict DNA behavior under physiological conditions. Here we use an elastic rod model to predict the stability boundary (critical torque vs. applied tension) for single molecule DNA experiments in which the molecule is subjected to applied tension and twist. We discuss the shortcomings of the usual isotropic rod model. We then derive a consistent non-linear material law from the general representation for a hemitropic (chiral) rod. Finally, we present results of a standard bifurcation analysis predicting the stability boundary. We find results from the non-linear hemitropic rod to match the data closely.     

Effect of the Boundary Conditions and Influence of the Rotational Inertia on the Vibrational Modes of an Elastic Ring

We present the small-amplitude vibrations of a circular elastic ring with periodic and clamped boundary conditions. We model the rod as an inextensible, isotropic, naturally straight Kirchhoff elastic rod and obtain the vibrational modes of the ring analytically for periodic boundary conditions and numerically for clamped boundary conditions. Of particular interest are the dependence of the vibrational modes on the torsional stress in the ring and the influence of the rotational inertia of the rod on the mode frequencies and amplitudes. In rescaling the Kirchhoff equations, we introduce a parameter inversely proportional to the aspect ratio of the rod. This parameter makes it possible to capture the influence of the rotational inertia of the rod. We find that the rotational inertia has a minor influence on the vibrational modes with the exception of a specific category of modes corresponding to high-frequency twisting deformations in the ring. Moreover, some of the vibrational modes over or undertwist the elastic rod depending on the imposed torsional stress in the ring.     

Finite element,stream function-vorticity solution of secondary flow in the channels of a rod bundle

A finite element method has been applied to predict the overall features of the fully developed turbulent flow in the non-circular channels of a rod bundle. The finite element discretization is based on the conventional Galerkin method using an isoparametric quadrilateral element with mixed interpolation. The primary axial flow and turbulent kinetic energy distributions have been predicted for fully developed turbulent flow conditions right up to the wall. The secondary velocity is represented by the stream function-vorticity formulation and the no-slip boundary conditions are explicitly introduced in the nonlinear equations by a boundary vorticity formula. The Newton-Raphson method is applied to the stream function-vorticity equations and solved simultaneously by the frontal solution technique. A one-equation eddy viscosity model of turbulence and an algebraic stress transport model have been used to predict primary axial velocity, secondary velocities and turbulent kinetic energy. The predictions obtained for a central subchannel of an equilateral-triangular rod array with p/d= 1.3 are in reasonable agreement with experimental data.     

圆截面杆在曲线井中的屈曲问题

本文研究了线弹性的圆截面压杆在刚性井壁的曲线井中的屈曲问题。压杆两端为铰支，杆和井壁之间的摩擦力忽略不计，失稳前假设压杆位于曲线井的较低侧。分析了压杆屈曲时的几何变形条件，导出了压杆的曲率，变形能和各项外力势的表达式，用最小势能原理导出压杆失稳的微分方程和边界条件。引入梁单元，用有限单元法求得了压杆失稳时的临界压力和杆轴线状态。结果显示，临界压力随着压杆自重和曲线井半径的增加而增加。自重为零时，杆轴线为半个正弦曲线；自重不为零时，杆轴线为振荡的曲线，且振荡主要集中在压杆顶部。     

On the derivation of an admissibility condition for phase boundary propagation in an SMA bar based on a 3-D formulation

There is some considerable difficulty in determining the solution uniquely for a propagating phase boundary in shape memory alloy (SMA) bar. In this paper, we establish an admissibility condition starting from a three-dimensional (3-D) internal-variable formulation to resolve this issue. We adopt a 3-D formulation in literature which is based on a constitutive model with specific forms of the Helmholtz free energy and dissipation rate. Then the 3-D dynamical equations are reduced to the 1-D rod equations for three phase regions (coupled with the radial effect and surface condition) by using two small parameters. Connection conditions at the phase interfaces are determined. By considering the traveling-wave solution for the rod system, we eventually derive three conditions across a sharp phase boundary corresponding to the 1-D sharp-interface model, including the two usual jump conditions and an additional condition. The third condition is then used to supplement the 1-D sharp-interface model to study an impact problem. The unique solution is constructed analytically for all possible impact velocity, including three kinds of wave patterns according to different levels of the impact velocity. The results are compared with those obtained by the maximal dissipation rate criterion.     

The role of divergent terms in the Frank energy of nematic liquid crystals

The effect of divergent terms in the Frank orientation energy of nematic liquid crystals on the equilibrium state of the director field is studied. Such terms have no effect on the equations of motion or on the equilibrium of the medium under consideration; however, they should be taken into account in the derivation of boundary conditions. It is shown that, in the case of boundary perturbations or in the case of polar orientation angle perturbations, the divergent terms can be considered as a surface energy for the azimuth angle (this energy is similar to the Rapini-Papoular energy). In addition, these terms may cause a deviation of the director in the plane parallel to the boundary. The equilibrium problem for a nematic liquid crystal is considered as an example in the case of small periodic boundary perturbations.     

井筒内受压杆管后屈曲能量法分析与实验研究

目前不少理论力学教材都涉及刚体平面运动动力学方程的教学内容,但有些教材在叙述上有许多值得商榷之处.对这一重要的基本概念,本文提出作者的思考,供理论力学教学的教师与学过此内容的学生讨论.     

Helical buckling of a whirling conducting rod in a uniform magnetic field

We study the effect of a magnetic field on the behaviour of a conducting elastic rod subject to a novel set of boundary conditions that, in the case of a transversely isotropic rod, give rise to exact helical post-buckling solutions. The equations used are the geometrically exact Kirchhoff equations and both static (buckling) and dynamic (whirling) instability are considered. Critical loads are obtained explicitly and are given by a surprisingly simple formula. By solving the linearised equations about the (quasi-)stationary solutions we also find secondary instabilities described by (Hamiltonian-)Hopf bifurcations, the usual signature of incipient ‘breathing’ modes. The boundary conditions can also be used to generate and study helical solutions through traditional non-magnetic buckling due to compression, twist or whirl.     

Linear water wave propagation through multiple floating elastic plates of variable properties

We investigate the problem of linear water wave propagation under a set of elastic plates of variable properties. The problem is two-dimensional, but we allow the waves to be incident from an angle. Since the properties of the elastic plates can be set arbitrarily, the solution method can also be applied to model regions of open water as well as elastic plates. We assume that the boundary conditions at the plate edges are the free boundary conditions, although the method could be extended straightforwardly to cover other possible boundary conditions. The solution method is based on an eigenfunction expansion under each elastic plate and on matching these expansions at each plate boundary. We choose the number of matching conditions so that we have fewer equations than unknowns. The extra equations are found by applying the free-edge boundary conditions. We show that our results agree with previous work and that they satisfy the energy balance condition. We also compare our results with a series of experiments using floating elastic plates, which were performed in a two-dimensional wave tank.     

Study of static and dynamic stability of flexible rods in a geometrically nonlinear statement

We study static and dynamic stability problems for a thin flexible rod subjected to axial compression with the geometric nonlinearity explicitly taken into account. In the case of static action of a force, the critical load and the bending shapes of the rod were determined by Euler. Lavrent’ev and Ishlinsky discovered that, in the case of rod dynamic loading significantly greater than the Euler static critical load, there arise buckling modes with a large number of waves in the longitudinal direction. Lavrent’ev and Ishlinsky referred to the first loading threshold discovered by Euler as the static threshold, and the subsequent ones were called dynamic thresholds; they can be attained under impact loading if the pulse growth time is less than the system relaxation time. Later, the buckling mechanism in this case and the arising parametric resonance were studied in detail by Academician Morozov and his colleagues.In this paper, we complete and develop the approach to studying dynamic rod systems suggested by Morozov; in particular, we construct exact and approximate analytic solutions by using a system of special functions generalizing the Jacobi elliptic functions. We obtain approximate analytic solutions of the nonlinear dynamic problem of flexible rod deformation under longitudinal loading with regard to the boundary conditions and show that the analytic solution of static rod system stability problems in a geometrically nonlinear statement permits exactly determining all possible shapes of the bent rod and the complete system of buckling thresholds. The study of approximate analytic solutions of dynamic problems of nonlinear vibrations of rod systems loaded by lumped forces after buckling in the deformed state allows one to determine the vibration frequencies and then the parametric resonance thresholds.     

非局部杆纵向振动的特性研究

基于非局部理论，研究弹性杆在任意边界约束条件下的纵向振动特性．根据Chebyshev 谱级数建立非局部弹性杆的纵向位移形式．在杆的两端引入纵向约束弹簧，通过设置弹簧刚度系数，模拟经典边界及弹性边界．建立非局部杆的能量表达式，由瑞利-里兹法得到齐次线性方程组，求解对应的矩阵特征值与特征向量问题获得非局部杆的固有频率和振型．通过数值仿真计算，研究非局部特征系数与边界约束条件对非局部杆振动频率的影响．结果表明本文方法合理简便，具有良好的精度，且适用于任意弹性边界条件．     

Improving the differentiability of generalized fourier series solutions of boundary value problems of mechanics by using boundary functions

We prove a theorem on conditions for the differentiation of generalized Fourier series. We show that Fourier series solutions of boundary value problems can in general be differentiated term by term only once. To improve the differentiability properties of such series, we suggest to use pth-order boundary functions. We suggest an algorithm for constructing boundary functions for classical domains. This approach is illustrated by a new solution, with improved differentiability properties, of the problem on the torsion of an elastic rod of rectangular cross-section.     

Distributed-order fractional wave equation on a finite domain: creep and forced oscillations of a rod

We study waves in a rod of finite length with a viscoelastic constitutive equation of distributed fractional order type for the special choice of weight functions. Prescribing boundary conditions on displacement and stress, we obtain, as special solutions, cases corresponding to creep and forced oscillations. In solving system of differential and integro-differential equations, we use the Laplace transformation in the time domain.     

Anomalous dependence of the vibration frequencies of a rod in an elastic medium on the rod length

We use numerical-analytic methods to study the influence of the length of a thin inhomogeneous rod on its natural frequencies and the shapes of its plane transverse vibrations. We found that the existence of an external elastic medium described by the Winkler model can lead to an anomalous effect, i.e., to an increase in the natural frequencies of the vibration lower modes as the rod length increases continuously. We discovered rather subtle properties of this phenomenon in the case of variations in the length, the mode number, and the fixation method. We separately studied vibrations for the standard boundary conditions: fixation, hinged fixation, tangential fixation, and free end. We calculated several simple examples illustrating the anomalous dependence of the frequency of the rod natural vibrations in a strongly inhomogeneous elastic medium with different boundary conditions.     

On the solution of boundary value problems of mechanics for the Poisson equation and related equations

To a boundary value problem, we assign an auxiliary problem of determining the spectrum of eigenfunctions and eigenvalues (EFV). After the main problem has been reduced to a form with homogeneous boundary conditions, it becomes possible to prove theorems about the formulas for the solution of the boundary value problem with linear equations of elliptic type for multidimensional multiply connected domains by using the spectral expansion in the Fourier series. We find conditions under which the action of second-order differential operators on the obtained solutions in the Fourier series can be computed not only in the interior of the domain but also on its boundary. But if these conditions are not satisfied, then the series for second-order differential operators do not converge on the boundary. The proposed method for the expansion in the EFV can be used not only in plane but also in spatial problems if the domain of complicated shape can be represented as a combination of bounded domains with known EFV spectra. As one of the examples, we consider the problem of torsion of an elastic rod whose cross-section consists of a rectangle and a half-disk.     

Transverse-longitudinal bending of rheonomic rods

In [1, 2], an energy method for the determination of critical buckling times is developed for rods subjected to compression in the conditions of longitudinal bending. In this case, for given compressive loads, the bending moments in the rod cross-sections depend only on the current deflection of the rod axis. In contrast to longitudinal bending, in the case of transverse-longitudinal bending the bending moment in general depends not only on the deflection but also on the axial coordinate and the reaction forces in the supports. Depending on the rod fixing conditions, the problems of transverse-longitudinal bending can be categorized as statically determinate or statically indeterminate. In the latter case, the derivation of equilibrium conditions for a rod segment is complicated by the indefiniteness of the reactions in the rod buckling process. In the current paper, the energy method developed in [1, 2] is extended to a class of statically indeterminate transverse-longitudinal bending problems. To determine the redundant variables, it is proposed to use the principle of minimum of additional dissipation.     

Wave propagation in a piezoelectric rod of 6 mm symmetry

The wave propagation in a piezoelectric rod of 6 mm symmetry is investigated by applying a 3-D piezoelectric elastic model. A self-adjoint method is introduced to solve this problem, this method avoids calculating the generalized eigenvalue equation, it completely draws the dispersion curves in the forms of Quasi-P wave, Quasi-SV wave and Quasi-SH wave under the self-adjoint boundary condition, and it can evaluate the dispersion curves of all kinds of boundary conditions. As an example, the dispersion curves of PLT-5H are completely drawn, we also found the Quasi-SV wave has standing wave phenomenon in the PLT-5H rod. In addition the relation of dispersion curves among different boundary conditions is discussed, and an experiment method is introduce to decide the dispersion curves for another boundary conditions.     

Thermally generated stress waves in a dispersive elastic rod

The propagation of thermally generated stress waves in a dispersive elastic rod was investigated both experimentally and analytically. In the experimental investigation, the end of a circular colored-glass rod was heated very rapidly by the deposition of luminous energy from a Q-switched ruby laser. The light from the laser was directed parallel to the axis of the rod and deposited on the polished end of the rod. The depth of deposition was of the same order as the radius of the rod. The length of the energy pulse from the laser was 20 nsec. This results in heating at such a rate that it can be considered as instantaneous when compared to the mechanical response of the material used. The resulting stress wave was measured using a thin quartz crystal in a Hopkinson pressure-bar arrangement. Radial inertia precluded the use of the simple wave equation; Love's modified wave equation was used to describe the motion. The thermoelastic problem was reduced to a homogeneous partial differential equation with appropriate initial and boundary conditions which is solved by the separation of variables technique. The experimental results are in good agreement with Love's theory. The amplitude of the stress waves was found to be directly proportional to the total energy deposited. The very short stress pulses generated by Q-switched laser deposition on the end of the thin rod gave rise to the higher modes of longitudinal wave propagation. The existence of wave propagation in a thin rod at near dilatational velocities was experimentally confirmed. It is concluded that the experimental techniques developed can be used to model stress-wave generation due to electromagnetic-energy depositions. Also, laser deposition provides an efficient means for generating the higher modes of longitudinal wave propagation in thin rods. Paper was presented at 1968 SESA Spring Meeting held in Albany, N. Y., on May 7–10. This work was supported by the U. S. Atomic Energy Commission at University of California, Lawrence Radiation Laboratory, Livermore, Calif.     

Reply to Comments on “Non-Darcian Forced Convection Flow of Viscous Dissipating Fluid over a Flat Plate Embedded in a Porous Medium”

In this note, we reply to the comments by Rees and Magyari (2007) on our article (Aydin and Kaya 2007). They mainly stated that the thermal boundary conditions we defined at the edge of the boundary layer were incompatible with the energy equation. This is questionable and therefore we will discuss it below. They disclosed that our results were in error. However, this is quite misleading. Scientifically, they cannot reach such a conclusion without comparing our results with what they thought to be correct. In fact, this misleading and unproven statement will be shown not to be correct in the following.     

Non-linear dynamic intertwining of rods with self-contact

Twisted marine cables on the sea floor can form highly contorted three-dimensional loops that resemble tangles. Such tangles or ‘hockles’ are topologically equivalent to the plectomenes that form in supercoiled DNA molecules. The dynamic evolution of these intertwined loops is studied herein using a computational rod model that explicitly accounts for dynamic self-contact. Numerical solutions are presented for an illustrative example of a long rod subjected to increasing twist at one end. The solutions reveal the dynamic evolution of the rod from an initially straight state, through a buckled state in the approximate form of a helix, through the dynamic collapse of this helix into a near-planar loop with one site of self-contact, and the subsequent intertwining of this loop with multiple sites of self-contact. This evolution is controlled by the dynamic conversion of torsional strain energy to bending strain energy or, alternatively, by the dynamic conversion of twist (Tw) to writhe (Wr).